Rare Alleles and a Recent Population Bottleneck

I remember hearing something about the distribution of rare alleles being a problem for a recent bottleneck. Am I remembering this correctly, and are there any references anyone would recommend for the pop gen newbies?


Yes, that is likely true, but different than what we are discussing here. @glipsnort emphasizes the distribution of rare alleles in his work on AFS/SFS. You can learn about it from this 2016 thread: Can someone explain like I'm 5 yo, what's wrong with this refutation of Biologos? - Scientific Evidence - The BioLogos Forum.

You’ll quickly see how much our understanding has grown since then. There are some questions about whether or not that result holds up in a YEC model with a population that is always exponentially growing. In contrast, @glipsnort’s simulations used a constant population size. Moreover, @agauger has published simulations that suggests varying population size can reproduced the right distribution with an origin 200,000 years ago, but those results have not been confirmed.

Note: the comment about 200 kya was shown to be suspect.

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My population size increased exponentially until a fairly large size, and was then constant.

Where have they been published? The only simulation I’ve seen from her got sort of the right distribution with an origin 500 kya, as I recall.


It can be hard to keep track of it all. Remember this one? Gauger: A Single-Couple Human Origin is Possible.

Thank’s for the clarification. The amount of time spent in exponential growth phase during the simulation is quite low. That is the issue that Sanford/Carter have disputed, and that @Agauger relaxes by considering a time-variable population size.

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Yes, that’s the 500 kya one I was referring to. They say in the abstract that they think they could make 100 kya work but provide zero support for that statement.


The provide no support for 100 kya, but I was under the impression that they did show support for 200 kya. I have not recently reviewed the paper. Is my recollection mistaken?

I believe so. I don’t have time to read it again in detail, but I recall only 500 kya being modeled.


They modelled 2 scenarios: the first was Adam and Eve 2 million years ago, and the second was an Adam and Eve with some amount of created heterozygosity 500,000 years ago.


Thank you. If that’s correct, I was in error, and may have been thinking of some unpublished work I have seen.

From the abstract:

We show that a single-couple origin of humanity as recent as 500kya is consistent with data. With only minor modifications of our parsimonious model assumptions, we suggest that a single-couple origin 100kya, or more recently, is possible

From the methods:

Scenario 1 A single couple 100,000 generations ago (about 2mya) having zero heterozygosity (identical homozygous chromosomes), grows rapidly to a population of 10,000 people, then grows slowly and linearly to 16,000 people near the present.

Scenario 2 A single couple 25,000 generations ago (about 500kya) having primordial heterozygosity of 0.012,5 grows rapidly to a population of 16,000 people, then holds steady.

And the discussion:

First, the most obvious extension of our model is to generalize the parameter that (apart from primordial diversity) determines the timescale - the germline mutation rate.

As a second extension, it is worth noting that the human population has probably been very nonhomogeneous, with several more or less interconnected subpopulations, which could skew the distribution of alleles

The third and possibly most promising extension of our model is to include natural selection, most notably directional selection with selective sweeps.

But in light of the many possible extensions, we suggest that it is possible to fit a model to genetic data, for which the founding couple lived 100kya ago or even more recently.

That 100 kya is unsubstantiated speculation, and perhaps should not have been included in the abstract.

Their conclusion is:

the critical point that we wish to make is that, as far as we know scientifically from the genetic data, the human species could have come from as a single couple, so that all humans alive today could have descended uniquely from that first pair.

It is notable that this paper does not address all the genetic data, but only one narrow dimension. So this conclusion is not appropriately qualified. They only showed this with AFS/SFS, not other aspects of the data, such as TMR4A. In light of my reread of the paper, it seems that this does not add new information to @glipsnort’s analysis in 2016.

It appears also that @glipsnort and @evograd were correct. They did not consider a scenario with AE 200 kya. Thank you for the correction.

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Thanks for finding that old thread, and a belated thanks to @glipsnort for slogging through that data 4 years ago!! The figures at the end of the thread are really interesting, as is the concept for the models.

From the thread:

Conventional model:

YEC model:

What the models demonstrate is that there hasn’t been enough time to produce thousands of rare (~5% of the population) variants in each genome.



Using your own criteria, aren’t we compelled to say this conclusion is completely fallacious because it doesn’t specify the time frame … in fact the abstract seems to go out of its way to further muddle the timeframe issues?

@sfmatheson has convinced me that “Fallacious” is not the right term.

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